With 1.13, Minecraft made their data storing system (Named Binary Tag) accessible by the in-game player, outside of the entity/item creation.

[Added] An nbt argument in target selectors.

With such features being added, I am questioning if the Bukkit/Spigot guideline still holds up

If your change revolves around an implementation detail then it is not proper API design. Examples of bad API design would be along the lines of a packet API or an NBT storage API.

The packets are still something that is "invisible" to the normal Minecraft player, but NBT tags and their value have grown in usage with the last couple of updates.

Besides those "design choices", such API would finally enable data storage on items without having to store it in the lore. 

Obviously, this is purely a "choice" to make. If whoever will respond to my suggestion believes that such API is still bad practice and should not be implemented, I also accept that opinion, just something I wanted to throw here